/*
* SingleTipObservationProcess.java
*
* Copyright (c) 2002-2016 Alexei Drummond, Andrew Rambaut and Marc Suchard
*
* This file is part of BEAST.
* See the NOTICE file distributed with this work for additional
* information regarding copyright ownership and licensing.
*
* BEAST is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as
* published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* BEAST is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with BEAST; if not, write to the
* Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
* Boston, MA 02110-1301 USA
*/
package dr.evomodel.MSSD;
import dr.evomodel.siteratemodel.SiteRateModel;
import dr.evolution.alignment.PatternList;
import dr.evolution.util.Taxon;
import dr.evomodel.branchratemodel.BranchRateModel;
import dr.evomodel.tree.TreeModel;
import dr.inference.model.Parameter;
/**
* Package: SingleTipObservationProcess
* Description:
* <p/>
* <p/>
* Created by
* Alexander V. Alekseyenko (alexander.alekseyenko@gmail.com)
* Date: Feb 19, 2008
* Time: 2:57:14 PM
*/
public class SingleTipObservationProcess extends AnyTipObservationProcess {
protected Taxon sourceTaxon;
public SingleTipObservationProcess(TreeModel treeModel, PatternList patterns, SiteRateModel siteModel,
BranchRateModel branchRateModel, Parameter mu, Parameter lam, Taxon sourceTaxon) {
super("SingleTipObservationProcess", treeModel, patterns, siteModel, branchRateModel, mu, lam);
this.sourceTaxon = sourceTaxon;
}
public double calculateLogTreeWeight() {
return -lam.getParameterValue(0) / (getAverageRate() * mu.getParameterValue(0));
}
}